Phylogenetic relationships of 
            Chacodelphys
             (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences

Abstract Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved. Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.

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A Phylogenetic Investigation of the New Zealand Pteridaceae Ferns

10.26686/wgtn.16934449.v1 ◽

2021 ◽

Author(s):

◽

Whitney L M Bouma

Keyword(s):

New Zealand ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Native Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Taxonomic Confusion ◽

Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

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Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

Antarctic Science ◽

10.1017/s0954102009990253 ◽

2009 ◽

Vol 21 (6) ◽

pp. 565-570 ◽

Cited By ~ 15

Author(s):

Kristen L. Kuhn ◽

Thomas J. Near

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Single Copy ◽

Morphological Characters ◽

Mitochondrial Genes ◽

Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

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Phylogenetic relationships of Nygolaimina and Dorylaimina (Nematoda: Dorylaimida) inferred from small subunit ribosomal DNA sequences

Nematology ◽

10.1163/1568541054192199 ◽

2005 ◽

Vol 7 (1) ◽

pp. 59-79 ◽

Cited By ~ 35

Author(s):

Peter G. Mullin ◽

Timothy S. Harris ◽

Thomas O. Powers

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Sister Taxon ◽

Monophyletic Lineage ◽

Rdna Sequence Data ◽

The Common ◽

Small Subunit Ribosomal Dna ◽

18S Rdna Sequence

Abstract Phylogenetic reconstructions based on 18S rDNA sequence data indicate that Dorylaimida, comprising the suborders Nygolaimina and Dorylaimina, is a monophyletic lineage, but that there is a deep division within Nygolaimina, giving rise to the possibility that Nygolaimina is paraphyletic. A well-supported clade comprising members of the traditional orders Mermithida and Mononchida (including Bathyodontina) forms the sister taxon to the Dorylaimida. Inferred relationships within this clade indicate that Mermithida shares more recent common ancestry with Mononchina than does Bathyodontina. Vertebrate parasites within Dorylaimia (Dioctophymida and Trichinellida) are reconstructed in a sister-taxon relationship with the Mononchida/Dorylaimida lineage. The enigmatic order Isolaimida (represented by Isolaimium) appears to be ancestral to all other Dorylaimia sampled. Expanded taxon sampling for phylogenetic analyses of the subclass raises new possibilities for the reconstruction of hypothetical character states in the common ancestor of Dorylaimia.

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A Phylogenetic Investigation of the New Zealand Pteridaceae Ferns

10.26686/wgtn.16934449 ◽

2021 ◽

Author(s):

◽

Whitney L M Bouma

Keyword(s):

New Zealand ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Native Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Taxonomic Confusion ◽

Species Specific

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Placing ancient DNA sequences into reference phylogenies

10.1101/2020.12.19.423614 ◽

2020 ◽

Author(s):

Rui Martiniano ◽

Bianca De Sanctis ◽

Pille Hallast ◽

Richard Durbin

Keyword(s):

Ancient Dna ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Current Standard ◽

Phylogenetic Placement ◽

Target Capture ◽

Y Chromosomes ◽

Sequencing Studies ◽

Low Coverage

AbstractDuring the last decade, large volumes of ancient DNA (aDNA) data have been generated as part of whole-genome shotgun and target capture sequencing studies. This includes sequences from non-recombining loci such as the mitochondrial or Y chromosomes. However, given the highly degraded nature of aDNA data, post-mortem deamination and often low genomic coverage, combining ancient and modern samples for phylogenetic analyses remains difficult. Without care, these factors can lead to incorrect placement.For the Y chromosomes, current standard methods focus on curated markers, but these contain only a subset of the total variation. Examining all polymorphic markers is particularly important for low coverage aDNA data because it substantially increases the number of overlapping sites between present-day and ancient individuals which may lead to higher resolution phylogenetic placement. We provide an automated workflow for jointly analysing ancient and present-day sequence data in a phylogenetic context. For each ancient sample, we effectively evaluate the number of ancestral and derived alleles present on each branch and use this information to place ancient lineages to their most likely position in the phylogeny. We provide both a parsimony approach and a highly optimised likelihood-based approach that assigns a posterior probability to each branch.To illustrate the application of this method, we have compiled and make available the largest public Y-chromosomal dataset to date (2,014 samples) which we used as a reference for phylogenetic placement. We process publicly available African ancient DNA Y-chromosome sequences and examine how patterns of Y-chromosomal diversity change across time and the relationship between ancient and present-day lineages. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.

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Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽

10.1515/mammalia-2017-0081 ◽

2019 ◽

Vol 83 (2) ◽

pp. 180-189 ◽

Cited By ~ 2

Author(s):

Adam W. Ferguson ◽

Houssein R. Roble ◽

Molly M. McDonough

Keyword(s):

Phylogenetic Relationships ◽

Sequence Data ◽

Alternative Hypothesis ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Sister Relationship ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Molecular Phylogenetic ◽

Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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Pyrenochaetopsis kuksensis (Pyrenochaetopsidaceae), a new species associated with an ornamental boxwood in the Czech Republic

Phytotaxa ◽

10.11646/phytotaxa.498.3.3 ◽

2021 ◽

Vol 498 (3) ◽

pp. 177-185

Author(s):

MILAN ŠPETÍK ◽

AKILA BERRAF-TEBBAL ◽

ROBERT POKLUDA ◽

ALEŠ EICHMEIER

Keyword(s):

Czech Republic ◽

New Species ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Phylogenetic Analyses ◽

New Taxon ◽

The Czech Republic ◽

Buxus Sempervirens ◽

Fungal Microbiome ◽

A New Species

During the investigation of fungal microbiome associated with boxwood in the Czech Republic, samples from Buxus sempervirens L. (Buxaceae) plants were collected and used for isolation. Two fungal strains were proposed as a new species Pyrenochaetopsis kuksensis based on morphology as well as phylogenetic analyses of ITS, LSU, rpb2, and tub2 sequence data. Detailed descriptions and phylogenetic relationships of the new taxon are provided.

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Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)

Parasites & Vectors ◽

10.1186/s13071-020-04430-6 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Yi-Fan Cao ◽

Hui-Xia Chen ◽

Yang Li ◽

Dang-Wei Zhou ◽

Shi-Long Chen ◽

...

Keyword(s):

New Species ◽

Ribosomal Dna ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Small Subunit ◽

Sister Relationship ◽

Tibetan Antelope ◽

A New Species

Abstract Background The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered species of mammal endemic to the Qinghai-Tibetan Plateau. Parasites and parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites of the Tibetan antelope remains limited. Methods Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens was observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences, i.e. small subunit ribosomal DNA (18S), large subunit ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 (cox1), were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox1 sequence data, respectively, in order to clarify the systematic status of these nematodes. Results Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum (Oxyurida: Oxyuridae). There was no intraspecific nucleotide variation between different individuals of S. longicaudatum n. sp. in the partial 18S, 28S, ITS and cox1 sequences. However, a high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results suggest that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, as it formed a sister relationship to the genus Oxyuris. Conclusions A new species of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) is described. Skrjabinema longicaudatum n. sp. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to the knowledge of the species diversity of parasites from the Tibetan antelope, and clarify the systematic position of the genus Skrjabinema.

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Phylogenetic relationships of captorhinomorph reptiles

Canadian Journal of Earth Sciences ◽

10.1139/e86-042 ◽

1986 ◽

Vol 23 (3) ◽

pp. 402-418 ◽

Cited By ~ 40

Author(s):

M. J. Heaton ◽

R. R. Reisz

Keyword(s):

Phylogenetic Relationships ◽

Morphological Character ◽

Sister Taxon ◽

Morphological Pattern ◽

Natural Group

The Captorhinomorpha consists of two families, the Captorhinidae and the Protorothyrididae. The distribution of morphological character states of the skeleton permits reevaluation of currently accepted theories of the relationships of captorhinomorph reptiles. Identification of characters states that are primitive for reptiles (amniotes) has been made through outgroup comparison. The Captorhinidae, Protorothyrididae, and Diapsida form a natural group that share such derived characters as reduced supratemporal, reduced tabular, narrow supraoccipital with anteriorly directed crista alaris, loss of supratemporal–postorbital contact, loss of opisthotic–tabular contact, and loss of the medial centralia pedis. These shared derived character states indicate that captorhinomorphs are not the sister taxon of all other reptiles but are advanced relative to pelycosaurs, pareiasaurs, and procolophonids. Protorothyridids share with diapsids such derived characters as short postorbital region of the skull, keeled anterior presacral pleurocentra, slender limbs, and long, slender feet. This distribution of character states indicates that protorothyridids are more closely related to diapsids than either of these taxa is to captorhinids.The morphological pattern of small, lightly built, agile insectivores, represented by protorothyridids and early diapsids, is no longer considered to be the primitive amniote condition. Available evidence indicates that the most primitive amniote adaptation was, instead, that of a small, relatively slow carnivore that probably fed on primitive, terrestrial annelids and arthropods.

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Strelitziana sarbhoyi sp. nov. (Strelitzianaceae, Chaetothyriales), from North-Western Himalayas, India, described based on morphology and molecular phylogeny

Phytotaxa ◽

10.11646/phytotaxa.427.1.6 ◽

2019 ◽

Vol 427 (1) ◽

pp. 51-59

Author(s):

SHIWALI RANA ◽

SANJAY KUMAR SINGH ◽

PARAS NATH SINGH

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Culture Collection ◽

Fungal Culture ◽

Western Himalayas ◽

Holotype Specimen ◽

North Western

Strelitziana sarbhoyi is established as a new species to accommodate a phylloplane fungus isolated from Mallotus philippensis collected from Kangra region of North-Western Himalayas, Himachal Pradesh. The identity of the fungus is confirmed based on the asexual-morphs, cultural characteristics and phylogenetic analyses of the internal transcribed spacer (ITS) rDNA and partial nuclear ribosomal 28S large subunit (LSU) sequence data. The placement of S. sarbhoyi in the phylogenetic tree was determined based on DNA sequences from authenticated isolates of Strelitziana. Strelitziana sarbhoyi shows nearly 94% similarity with other known species of Strelitziana. Area description is provided for the proposed taxon along with microscopic images, and a phylogenetic tree. This is probably the first report of Strelitziana from India. Holotype specimen (dried voucher culture) is deposited in the Ajrekar Mycological Herbarium (AMH), and an ex-type culture is deposited in National Fungal Culture Collection of India (NFCCI).

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